Rates of C. diff and MRSA in elderly patients fell between October 2011 and September last year, the Healthcare Environ-ment Inspectorate (HEI) reported.
It conducted 31 insp-ections over the period and found hospitals to be "generally clean".
But it said more attention has to be paid to hard-to-reach areas such as under beds, on top of curtain rails and floor corners.
The cleaning of patient equipment should also be improved and cleaning schedules need to be properly filled out, the report said.
The HEI made 110 requirements and 81 recommendations for hospitals in the period, down from 172 requirements and 180 recommendations in the first report conducted in 2009-10.
Rates of C. diff among elderly patients fell by 37% and cases of MRSA fell by 35% over the same period.
Between December 2007 and June 2008, 55 patients developed C.diff at the Vale of Leven hospital in West Dun-bartonshire, in Scot-land's worst outbreak.
Nine died from the bug and it was a factor in another nine deaths. An inquiry has yet to be concluded.
Health Secretary Alex Neil said: "I am encouraged to see notable improvements in hospitals, but we are not complacent."